Seed there is good advice in this thread - both ways - advice for going and staying. I say you listen to your gut insticts. It sounds perhaps that your son's draft status may be leading to a sense of entitlement. There is none at the D1 level that I am aware of.
The best I can tell, the fall season is crucial for freshman. Some kids will call home and say something like "I am pitching well this fall, my ERA is 0.00 this fall" What they might not tell you is that many of them are being rocketed all over the place but just happen to be getting caught by people. Another kid might say "I am hitting over .400 this fall" Again, it is possible that many of the base hits are nubbers. Not suggesting anything about your son, but coaches tend to play people who can perform. It is possible that body language or some other implied cue gave the impression your son lacked confidence in some way. Also, some kids don't react well to failure. If you show attitude or poor body language when things don't go your way, it can affect the coach's confidence in some kid. When my son was not playing as a freshman, my advice to him was to assume that if his name was not on the lineup card, then he was not good enough. I would not entertain discussions about how well other kids were performing with him. If he is not playing, don't blame the coach, get better. Not suggesting the coach still might not be mistaken, but focus on those things he can control.